Key result
Rare SLC25A11 germline variant linked to ~50% lower tumor expression in Carney-Stratakis syndrome.
Why the study?
Carney-Stratakis syndrome is caused by germline pathogenic variants in SDH subunit genes, but additional genetic contributors remain to be identified.
Case Report (n=1)
The identification of a deleterious SLC25A11 germline variant in a patient with Carney-Stratakis syndrome suggests a novel genetic basis for the disease pathogenesis.
Background Carney-Stratakis syndrome (CSS), a rare condition characterized by paragangliomas and/or pheochromocytomas and gastrointestinal stromal tumors (GIST), is caused by germline heterozygous pathogenic variants in the succinate dehydrogenase subunit genes (SDHB, SDHC, SDHD). Methods Histological, genetic, and functional analyses were conducted in a 59-year-old female with CSS (9 cm left pheochromocytoma, 4.8 cm paraganglioma, and 9.3 cm GIST). Whole-exome sequencing (WES) of germline DNA paired with tumor DNA was performed. Results WES identified a rare heterozygous germline variant (c.293G>A/p.Arg98His) in the mitochondrial 2-oxoglutarate/malate carrier gene (SLC25A11). This variant, located in a highly conserved residue of the SLC25A11 mitochondrial carrier domain, is predicted to be deleterious in silico (REVEL score = 0.81). WES of pheochromocytoma, paraganglioma, and GIST did not reveal somatic pathogenic variants in genes previously associated with these tumors. A significant reduction in SLC25A11 expression was observed in the tumors of this patient with the SLC25A11 c.293G>A variant (0.69 ± 0.003) compared to tumors from cluster 1 (1.39 ± 0.45; P = 0.0229) and cluster 2 (1.79 ± 0.71; P = .0154). Consistent with the mRNA findings, SLC25A11 protein levels were markedly reduced in the pheochromocytoma and paraganglioma compared to other tumors. Negative staining for 5-hydroxymethylcytosine in all 3 tumors suggests a DNA hypermethylation profile characteristic of cluster 1A, despite normal SDHB expression levels. However, genome-wide copy number variation analysis did not reveal any loss of heterozygosity at the SLC25A11 locus. Conclusion The loss of SLC25A11 expression in tumors, the absence of somatic drivers, and the hypermethylation status strongly support the role of SLC25A11 in CSS pathogenesis.
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Freitas-Castro et al. (2025) conducted a case report in Carney-Stratakis syndrome (n=1). SLC25A11 germline variant (c.293G>A/p.Arg98His) vs. Tumors from cluster 1 and cluster 2 was evaluated on SLC25A11 expression in tumors (p=0.0229). A rare heterozygous germline variant in SLC25A11 (c.293G>A) was identified in a patient with Carney-Stratakis syndrome, associated with significantly reduced tumor SLC25A11 expression (P=0.0229).
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